ABSTRACT Particular class II human leukocyte antigen (HLA) alleles have been found to be major genetic risk factors in many skin and rheumatic diseases, but the mechanisms underlying the associations are unknown. The prevailing paradigm, which had been based on the MHC restriction paradigm four decades ago, postulates that allele-specific presentation of self or foreign antigens is the culprit; however, this hypothesis remains unverified to this day. The unconventional theory presented here postulates that in addition to presenting peptidic antigens to T cells, HLA-DR molecules express signal transduction ligands that interact with surface receptors and trigger allele-specific signaling events. Under certain environmental conditions or stochastic events, such interactions provoke aberrant cellular events that may increase the risk and/or severity of skin and rheumatic diseases. Based on structural, functional and evolutionary considerations, we propose here that a region on the HLA-DR beta chain, called `cusp' - based on its crystal structure conformation - hosts allele-specific signal transduction ligands. To examine the HLA Cusp theory, we propose to perform a set of experiments to validate key elements in this novel concept. In the 2-year discovery period (R61 phase) we will perform RNA sequencing of cells stimulated by synthetic peptides corresponding to cusp regions coded by representative HLA-DRB1alleles. This will be followed by bioinformatics analyses to determine cusp allele- specific signature transcriptomes and gene ontologies. Additionally, the same allele-specific cusp peptides will be immobilized on solid matrices; cell surface proteins will be allowed to interact with the ligands and eluates will be analyzed by mass spectrometry. Proteins of interest will be expressed and purified, and their interaction with the ligands will be validated by cell-free binding assays. Candidate pathways discovered during the two-year R61 phase will be functionally characterized during year-3 (R33 phase). Here, cusp- activated signal transduction pathways will be mapped, and their biologic significance will be determined in translational experimental settings. At the end of this 3-year project, it is expected that novel, or previously unrecognized, HLA-DRB1allele-coded cusp-activated pathways will have been identified. Due to the involvement of the MHC in diverse biologic processes on the one hand, and the enigmatic mechanistic basis of its association with many health traits and diseases on the other, functional validation of the HLA Cusp theory could have a transformative effect.